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Summary

This concise, introductory text focuses on the basic principles of biochemistry, filling the gap between the encyclopedic volumes and the cursory overview texts.Principles of Biochemistry, 4/ehas a well-deserved reputation for being the most accurate biochemistry textbook in the market. Widely praised in its previous edition for currency, and clarity of exposition, the new edition has been thoroughly revised and updated to reflect recent changes in this dynamic discipline.

Table of Contents

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Preface

xxv

PART ONE Introduction

Introduction to Biochemistry

1

(25)

Biochemistry Is a Modern Science

2

(1)

The Chemical Elements of Life

3

(2)

Many Important Macromolecules Are Polymers

5

(6)

Proteins

6

(1)

Polysaccharides

7

(2)

Nucleic Acids

9

(1)

Lipids and Membranes

10

(1)

The Energetics of Life

11

(4)

Reaction Rates and Equilibria

12

(1)

Thermodynamics

13

(2)

Equilibrium Constants and Standard Gibbs Free Energy Changes

15

(1)

Biochemistry and Evolution

15

(1)

The Cell Is the Basic Unit of Life

16

(1)

Prokaryotic Cells: Structural Features

17

(1)

Eukaryotic Cells: Structural Features

18

(4)

The Nucleus

18

(1)

The Endoplasmic Reticulum and Golgi Apparatus

19

(1)

Mitochondria and Chloroplasts

20

(1)

Specialized Vesicles

21

(1)

The Cytoskeleton

22

(1)

A Picture of the Living Cell

22

(2)

Biochemistry Is Multidisciplinary

24

(2)

Appendix: The Special Terminology of Biochemistry

24

(1)

Selected Readings

25

(1)

Water

26

(26)

The Water Molecule Is Polar

27

(1)

Hydrogen Bonding in Water

28

(2)

Water Is an Excellent Solvent

30

(2)

Ionic and Polar Substances Dissolve in Water

30

(1)

Cellular Concentrations and Diffusion

31

(1)

Osmotic Pressure

31

(1)

Nonpolar Substances Are Insoluble in Water

32

(1)

Noncovalent Interactions

33

(3)

Charge--charge Interactions

33

(1)

Hydrogen Bonds

34

(1)

Van der Waals Forces

35

(1)

Hydrophobic Interactions

36

(1)

Water Is Nucleophilic

36

(1)

Ionization of Water

37

(2)

The pH Scale

39

(2)

Box 2.1 The little ``p'' in pH.

40

(1)

Acid Dissociation Constants of Weak Acids

41

(5)

Buffered Solutions Resist Changes in pH

46

(6)

Summary

49

(1)

Problems

49

(2)

Selected Readings

51

(1)

PART TWO Structure and Function

Amino Acids and the Primary Structures of Proteins

52

(32)

General Structure of Amino Acids

53

(2)

Structures of the 20 Common Amino Acids

55

(6)

Box 3.1 An Alternative Nomenclature

56

(1)

Aliphatic R Groups

57

(1)

Box 3.2 Common Names of Amino Acids

57

(1)

Aromatic R Groups

58

(1)

Sulfur-Containing R Groups

58

(1)

Side Chains with Alcohol Groups

59

(1)

Basic R Groups

59

(1)

Acidic R Groups and Their Amide Derivatives

60

(1)

The Hydrophobicity of Amino Acid Side Chains

60

(1)

Other Amino Acids and Amino Acid Derivatives

61

(1)

Ionization of Amino Acids

62

(4)

Peptide Bonds Link Amino Acids in Proteins

66

(1)

Protein Purification Techniques

67

(2)

Analytical Techniques

69

(3)

Amino Acid Composition of Proteins

72

(1)

Determining the Sequence of Amino Acid Residues

73

(2)

Protein Sequencing Strategies

75

(3)

Comparisons of the Primary Structures of Proteins Reveal Evolutionary Relationships

78

(6)

Summary

81

(1)

Problems

81

(2)

Selected Readings

83

(1)

Proteins: Three-Dimensional Structure and Function

84

(45)

There Are Four Levels of Protein Structure

86

(1)

Methods for Determining Protein Structure

87

(3)

The Conformation of the Peptide Group

90

(2)

The α Helix

92

(3)

β Strands and β Sheets

95

(2)

Loops and Turns

97

(1)

Teritary Structure of Proteins

98

(6)

Supersecondary Structures

99

(1)

Domains

100

(4)

Domain Structure and Function

104

(1)

Quaternary Structure

104

(3)

Protein Denaturation and Renaturation

107

(3)

Protein Folding and Stability

110

(5)

The Hydrophobic Effect

110

(1)

Hydrogen Bonding

111

(1)

Van der Waals Interactions and Charge--Charge Interactions

112

(1)

Protein Folding Is Assisted by Molecular Chaperones

112

(3)

Collagen, a Fibrous Protein

115

(1)

Structures of Myoglobin and Hemoglobin

116

(2)

Oxygen Binding to Myoglobin and Hemoglobin

118

(5)

Oxygen Binds Reversibly to Heme

118

(1)

Oxygen-Binding Curves of Myoglobin and Hemoglobin

119

(2)

Hemoglobin Is an Allosteric Protein

121

(2)

Antibodies Bind Specific Antigens

123

(6)

Summary

125

(1)

Problems

125

(2)

Selected Readings

127

(2)

Properties of Enzymes

129

(29)

The Six Classes of Enzymes

130

(2)

Kinetic Experiments Reveal Enzyme Properties

132

(3)

Chemical Kinetics

133

(1)

Enzyme Kinetics

134

(1)

The Michaelis--Menten Equation

135

(4)

Derivation of the Michaelis--Menten Equation

137

(1)

The Catalytic Constant kcat

138

(1)

The Meanings of Km

138

(1)

Kinetic Constants Indicate Enzyme Activity and Catalytic Proficiency

139

(1)

Measurement of Km and Vmax

140

(1)

Kinetics of Multisubstrate Reactions

141

(1)

Box 5.1 Hyperbolas versus Straight Lines

141

(1)

Reversible Enzyme Inhibition

142

(5)

Competitive Inhibition

143

(2)

Uncompetitive Inhibition

145

(1)

Noncompetitive Inhibition

146

(1)

Uses of Enzyme Inhibition

146

(1)

Irreversible Enzyme Inhibition

147

(1)

Allosteric Enzymes

148

(1)

Regulation of Enzyme Activity

148

(6)

Phosphofructokinase Is an Allosteric Enzyme

149

(1)

General Properties of Allosteric Enzymes

150

(2)

Two Theories of Allosteric Regulation

152

(1)

Regulation by Covalent Modification

153

(1)

Multienzyme Complexes and Multifunctional Enzymes

154

(4)

Summary

154

(1)

Problems

155

(2)

Selected Readings

157

(1)

Mechanisms of Enzymes

158

(34)

The Terminology of Mechanistic Chemistry

158

(2)

Nucleophilic Substitutions

159

(1)

Cleavage Reactions

160

(1)

Oxidation---Reduction Reactions

160

(1)

Catalysts Stabilize Transition States

160

(2)

Chemical Modes of Enzymatic Catalysis

162

(5)

Box 6.1 Site-Directed Mutagenesis Modifies Enzymes

163

(1)

Polar Amino Acid Residues in Active Sites

163

(1)

Acid-Base Catalysis

164

(1)

Covalent Catalysis

165

(1)

pH Affects Enzymatic Rates

166

(1)

Diffusion-Controlled Reactions

167

(4)

Triose Phosphate Isomerase

167

(3)

Superoxide Dismutase

170

(1)

Binding Modes of Enzymatic Catalysis

171

(7)

The Proximity Effect

172

(1)

Weak Binding of Substrates of Enzymes

172

(2)

Induced Fit

174

(1)

Transition-State Stabilization

175

(3)

Lysozyme

178

(4)

Box 6.2 Proposed Transition State for a Bimolecular Reaction

181

(1)

Properties of Serine Proteases

182

(10)

Zymogens Are Inactive Enzyme Precursors

182

(1)

Substrate Specificity of Serine Proteases

183

(1)

Serine Proteases Use Both the Chemical and the Binding Modes of Catalysis